Customers are cheered on by Apple workers as they are some of the first customers to buy the new iPhones at the Apple shop in Covent Garden, London. Photograph: John Stillwell/PA

Apple has been hit by shortages of its latest iPhone as its new flagship handset launched in the UK.

Mobile phone operator O2 was the worst affected by the supply problems. It confirmed that its stores did not have any stock of the 5S, Apple's top-of-the-range model , which features a fingerprint scanner and retails from £549.

Stock of the gold-coloured 5S sold out almost immediately at Apple's largest UK store in Covent Garden, London, where staff lined the entrance to applaud jubilant customers who had queued overnight to be among the first owners of the new handsets.

One shopper, who did not give his name, entered 30 minutes after the store opened to find the limited edition gold phones had already sold out.

"They haven't got gold in stock at the moment, but I can exchange [a standard] one for a gold one easily if I keep it sealed in the box." he said.

At Apple's Regent Street store, Noah Green, 17, was the first in the queue, having only left his vigil to shower at a nearby gym since setting up camp outside the store at 4pm on Monday. Emerging from the store 20 minutes after the doors opened to rapturous applause, clutching a gold 5S, he said: "It's the best feeling in the world. I'm the first in the United Kingdom and I have the best phone."

The teenager said he turned down offers of up to £5,000 for his prime spot in the queue, saying he would only consider giving up his place for £10,000.

A spokesperson for O2 said the company had made its 5S stock available in its online store, with the majority of models available for delivery within three to six weeks. "This is the first year we have chosen to put all our stock online and through our customer service due to the limited availability," said the O2 spokesperson. "Customers can also order in store but there will be a three to six week delay in receiving the phone – our stores will be in touch with the customer to confirm when their phone has come in."

Other mobile operators are also experiencing limited stock levels of the 5S. An EE spokesperson said there was limited supply.

"We're also expecting to receive further deliveries of stock soon, so customers who want the iPhone 5s on Orange or T-Mobile can place an order in store or with our telesales agents, who will contact them as soon as stock becomes available," the EE spokesperson added.

Vodafone also has stock, but it is being sold in all stores on a first-come, first-served basis, according to a company spokesperson. Three declined to comment on stock levels of the Apple's flagship phone, but confirmed on Twitter that the iPhone 5S was available both in-store and online.

Analysts said Apple tends to favour its own stores when allocating stock. "Apple has always prioritised stock for its own-brand stores to guarantee the strong Apple store brand and that customers can always come in and pick up the latest Apple hardware," said Ben Wood mobile analyst with research firm CCS Insight. "When Apple sells directly to the consumer its cutting out the middle man and therefore makes more money from sales through its own shops and online store."

However, Wood does not expect the stock shortages of the iPhone 5S to impact Apple in the long run: "Apple is exemplary on its logistics, and I can't foresee any longer term issues." The iPhone 5S and iPhone 5C launch marks the biggest in Apple's phone history, launching simultaneously in both traditional markets including the UK, US and Europe, as well as China and Japan among others.